graph-blast-bitscore.ipynb

{
 "metadata": {
  "name": "graph-blast-bitscore"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "# This is an IPython Notebook\n",
      "\n",
      "To run cells in this notebook, hold down the shift key and hit the Enter key (aka shift-Enter)"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ls /mnt"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "### For the next command, replace 'titus' with your own NetID "
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cd /mnt/titus"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "ls"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import csv\n",
      "r = csv.reader(open('salm.x.ecoli.csv', 'r'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "scores = []\n",
      "\n",
      "for row in r:\n",
      "    name1, descr1, name2, descr2, bitscore, evalue = row\n",
      "    bitscore = float(bitscore)\n",
      "    scores.append(bitscore)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print bitscore"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print name1, descr1, name2, descr2"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "hist(scores)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}